Sun 23 Dec 22:23:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmi-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-2.3-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-2.3-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:17 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-2.3-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 350 and 0 Target number of residues in the AU: 350 Target solvent content: 0.5801 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-2.3-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 87.180 2.320 Wilson plot Bfac: 45.01 20732 reflections ( 99.90 % complete ) and 0 restraints for refining 3163 atoms. Observations/parameters ratio is 1.64 ------------------------------------------------------ Starting model: R = 0.3403 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3161 (Rfree = 0.000) for 3163 atoms. Found 61 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.63 2.39 Round 1: 211 peptides, 30 chains. Longest chain 18 peptides. Score 0.511 Round 2: 248 peptides, 26 chains. Longest chain 28 peptides. Score 0.660 Round 3: 270 peptides, 23 chains. Longest chain 38 peptides. Score 0.736 Round 4: 262 peptides, 20 chains. Longest chain 41 peptides. Score 0.749 Round 5: 278 peptides, 21 chains. Longest chain 27 peptides. Score 0.768 Taking the results from Round 5 Chains 23, Residues 257, Estimated correctness of the model 92.1 % 9 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 52 A and 55 A Built loop between residues 268 A and 274 A 20 chains (265 residues) following loop building 6 chains (164 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 4097 restraints for refining 2687 atoms. 2483 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3106 (Rfree = 0.000) for 2687 atoms. Found 55 (60 requested) and removed 42 (30 requested) atoms. Cycle 2: After refmac, R = 0.2749 (Rfree = 0.000) for 2671 atoms. Found 41 (59 requested) and removed 33 (30 requested) atoms. Cycle 3: After refmac, R = 0.2692 (Rfree = 0.000) for 2648 atoms. Found 39 (58 requested) and removed 32 (30 requested) atoms. Cycle 4: After refmac, R = 0.2608 (Rfree = 0.000) for 2639 atoms. Found 22 (55 requested) and removed 31 (29 requested) atoms. Cycle 5: After refmac, R = 0.2552 (Rfree = 0.000) for 2614 atoms. Found 28 (54 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.60 2.37 Round 1: 280 peptides, 18 chains. Longest chain 55 peptides. Score 0.796 Round 2: 292 peptides, 16 chains. Longest chain 41 peptides. Score 0.827 Round 3: 300 peptides, 16 chains. Longest chain 51 peptides. Score 0.837 Round 4: 299 peptides, 15 chains. Longest chain 54 peptides. Score 0.842 Round 5: 308 peptides, 12 chains. Longest chain 54 peptides. Score 0.871 Taking the results from Round 5 Chains 13, Residues 296, Estimated correctness of the model 97.3 % 7 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 104 A Built loop between residues 199 A and 203 A 10 chains (301 residues) following loop building 5 chains (227 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 3436 restraints for refining 2690 atoms. 1434 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2467 (Rfree = 0.000) for 2690 atoms. Found 29 (54 requested) and removed 40 (30 requested) atoms. Cycle 7: After refmac, R = 0.2283 (Rfree = 0.000) for 2663 atoms. Found 21 (53 requested) and removed 32 (30 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 2642 atoms. Found 17 (51 requested) and removed 29 (29 requested) atoms. Cycle 9: After refmac, R = 0.2156 (Rfree = 0.000) for 2621 atoms. Found 15 (50 requested) and removed 29 (29 requested) atoms. Cycle 10: After refmac, R = 0.2159 (Rfree = 0.000) for 2599 atoms. Found 14 (48 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.59 2.36 Round 1: 305 peptides, 11 chains. Longest chain 86 peptides. Score 0.873 Round 2: 312 peptides, 8 chains. Longest chain 86 peptides. Score 0.896 Round 3: 313 peptides, 10 chains. Longest chain 86 peptides. Score 0.886 Round 4: 301 peptides, 14 chains. Longest chain 62 peptides. Score 0.851 Round 5: 309 peptides, 11 chains. Longest chain 57 peptides. Score 0.877 Taking the results from Round 2 Chains 9, Residues 304, Estimated correctness of the model 98.2 % 5 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 109 A Built loop between residues 180 A and 183 A Built loop between residues 215 A and 226 A Built loop between residues 298 A and 304 A 2 chains (322 residues) following loop building 1 chains (318 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2650 restraints for refining 2689 atoms. 221 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 2689 atoms. Found 48 (48 requested) and removed 38 (30 requested) atoms. Cycle 12: After refmac, R = 0.2071 (Rfree = 0.000) for 2689 atoms. Found 25 (47 requested) and removed 30 (30 requested) atoms. Cycle 13: After refmac, R = 0.1987 (Rfree = 0.000) for 2673 atoms. Found 36 (46 requested) and removed 30 (30 requested) atoms. Cycle 14: After refmac, R = 0.1915 (Rfree = 0.000) for 2673 atoms. Found 34 (44 requested) and removed 31 (30 requested) atoms. Cycle 15: After refmac, R = 0.1868 (Rfree = 0.000) for 2669 atoms. Found 32 (43 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.59 2.36 Round 1: 312 peptides, 8 chains. Longest chain 152 peptides. Score 0.896 Round 2: 312 peptides, 7 chains. Longest chain 82 peptides. Score 0.901 Round 3: 307 peptides, 10 chains. Longest chain 86 peptides. Score 0.881 Round 4: 308 peptides, 11 chains. Longest chain 61 peptides. Score 0.876 Round 5: 303 peptides, 14 chains. Longest chain 69 peptides. Score 0.853 Taking the results from Round 2 Chains 7, Residues 305, Estimated correctness of the model 98.3 % 6 chains (300 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 72 A Built loop between residues 105 A and 109 A Built loop between residues 165 A and 172 A Built loop between residues 217 A and 221 A Built loop between residues 301 A and 305 A 2 chains (323 residues) following loop building 1 chains (318 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2667 restraints for refining 2690 atoms. 234 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2297 (Rfree = 0.000) for 2690 atoms. Found 42 (42 requested) and removed 42 (30 requested) atoms. Cycle 17: After refmac, R = 0.2040 (Rfree = 0.000) for 2684 atoms. Found 28 (41 requested) and removed 30 (30 requested) atoms. Cycle 18: After refmac, R = 0.1967 (Rfree = 0.000) for 2678 atoms. Found 18 (40 requested) and removed 31 (30 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 2659 atoms. Found 19 (38 requested) and removed 29 (29 requested) atoms. Cycle 20: After refmac, R = 0.1887 (Rfree = 0.000) for 2645 atoms. Found 26 (37 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.59 2.36 Round 1: 309 peptides, 9 chains. Longest chain 78 peptides. Score 0.888 Round 2: 314 peptides, 10 chains. Longest chain 69 peptides. Score 0.887 Round 3: 315 peptides, 10 chains. Longest chain 75 peptides. Score 0.888 Round 4: 317 peptides, 7 chains. Longest chain 120 peptides. Score 0.905 Round 5: 303 peptides, 13 chains. Longest chain 55 peptides. Score 0.860 Taking the results from Round 4 Chains 7, Residues 310, Estimated correctness of the model 98.5 % 6 chains (306 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 101 A and 106 A Built loop between residues 224 A and 227 A Built loop between residues 243 A and 246 A Built loop between residues 295 A and 306 A 1 chains (326 residues) following loop building 1 chains (326 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2589 restraints for refining 2690 atoms. 114 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2198 (Rfree = 0.000) for 2690 atoms. Found 36 (36 requested) and removed 39 (30 requested) atoms. Cycle 22: After refmac, R = 0.1907 (Rfree = 0.000) for 2676 atoms. Found 35 (35 requested) and removed 31 (30 requested) atoms. Cycle 23: After refmac, R = 0.1814 (Rfree = 0.000) for 2672 atoms. Found 34 (34 requested) and removed 31 (30 requested) atoms. Cycle 24: After refmac, R = 0.1767 (Rfree = 0.000) for 2670 atoms. Found 32 (32 requested) and removed 30 (30 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1742 (Rfree = 0.000) for 2668 atoms. Found 31 (31 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.58 2.35 Round 1: 315 peptides, 10 chains. Longest chain 82 peptides. Score 0.888 Round 2: 320 peptides, 6 chains. Longest chain 118 peptides. Score 0.912 Round 3: 311 peptides, 7 chains. Longest chain 74 peptides. Score 0.901 Round 4: 312 peptides, 12 chains. Longest chain 87 peptides. Score 0.875 Round 5: 307 peptides, 10 chains. Longest chain 87 peptides. Score 0.881 Taking the results from Round 2 Chains 6, Residues 314, Estimated correctness of the model 98.7 % 5 chains (311 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 102 A Built loop between residues 218 A and 226 A Built loop between residues 248 A and 251 A Built loop between residues 300 A and 304 A 1 chains (326 residues) following loop building 1 chains (326 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2597 restraints for refining 2690 atoms. 122 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2111 (Rfree = 0.000) for 2690 atoms. Found 30 (30 requested) and removed 38 (30 requested) atoms. Cycle 27: After refmac, R = 0.1902 (Rfree = 0.000) for 2673 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 28: After refmac, R = 0.1805 (Rfree = 0.000) for 2670 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 29: After refmac, R = 0.1747 (Rfree = 0.000) for 2667 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 30: After refmac, R = 0.1731 (Rfree = 0.000) for 2659 atoms. Found 29 (29 requested) and removed 40 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.58 2.35 Round 1: 313 peptides, 9 chains. Longest chain 97 peptides. Score 0.892 Round 2: 319 peptides, 4 chains. Longest chain 133 peptides. Score 0.921 Round 3: 318 peptides, 6 chains. Longest chain 118 peptides. Score 0.911 Round 4: 312 peptides, 8 chains. Longest chain 154 peptides. Score 0.896 Round 5: 311 peptides, 11 chains. Longest chain 72 peptides. Score 0.879 Taking the results from Round 2 Chains 5, Residues 315, Estimated correctness of the model 98.9 % 4 chains (313 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 101 A and 106 A Built loop between residues 198 A and 201 A 1 chains (321 residues) following loop building 1 chains (321 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2650 restraints for refining 2690 atoms. 211 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2084 (Rfree = 0.000) for 2690 atoms. Found 30 (30 requested) and removed 38 (30 requested) atoms. Cycle 32: After refmac, R = 0.1864 (Rfree = 0.000) for 2674 atoms. Found 28 (30 requested) and removed 31 (30 requested) atoms. Cycle 33: After refmac, R = 0.1786 (Rfree = 0.000) for 2670 atoms. Found 25 (29 requested) and removed 29 (29 requested) atoms. Cycle 34: After refmac, R = 0.1781 (Rfree = 0.000) for 2656 atoms. Found 26 (29 requested) and removed 30 (29 requested) atoms. Cycle 35: After refmac, R = 0.1767 (Rfree = 0.000) for 2648 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.58 2.35 Round 1: 317 peptides, 7 chains. Longest chain 120 peptides. Score 0.905 Round 2: 318 peptides, 7 chains. Longest chain 108 peptides. Score 0.906 Round 3: 318 peptides, 8 chains. Longest chain 145 peptides. Score 0.901 Round 4: 308 peptides, 14 chains. Longest chain 72 peptides. Score 0.859 Round 5: 309 peptides, 11 chains. Longest chain 97 peptides. Score 0.877 Taking the results from Round 2 Chains 8, Residues 311, Estimated correctness of the model 98.5 % 6 chains (306 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 A and 109 A Built loop between residues 180 A and 183 A Built loop between residues 199 A and 203 A Built loop between residues 217 A and 226 A 2 chains (321 residues) following loop building 2 chains (321 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2643 restraints for refining 2690 atoms. 205 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2029 (Rfree = 0.000) for 2690 atoms. Found 30 (30 requested) and removed 40 (30 requested) atoms. Cycle 37: After refmac, R = 0.1817 (Rfree = 0.000) for 2674 atoms. Found 30 (30 requested) and removed 32 (30 requested) atoms. Cycle 38: After refmac, R = 0.1765 (Rfree = 0.000) for 2666 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 39: After refmac, R = 0.1735 (Rfree = 0.000) for 2664 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. Cycle 40: After refmac, R = 0.1713 (Rfree = 0.000) for 2660 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.58 2.35 Round 1: 311 peptides, 10 chains. Longest chain 76 peptides. Score 0.885 Round 2: 319 peptides, 5 chains. Longest chain 160 peptides. Score 0.916 Round 3: 315 peptides, 8 chains. Longest chain 143 peptides. Score 0.899 Round 4: 315 peptides, 8 chains. Longest chain 161 peptides. Score 0.899 Round 5: 312 peptides, 11 chains. Longest chain 130 peptides. Score 0.880 Taking the results from Round 2 Chains 5, Residues 314, Estimated correctness of the model 98.8 % 5 chains (314 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 171 A Built loop between residues 217 A and 221 A Built loop between residues 245 A and 248 A Built loop between residues 300 A and 304 A 1 chains (325 residues) following loop building 1 chains (325 residues) in sequence following loop building ------------------------------------------------------ 20732 reflections ( 99.90 % complete ) and 2637 restraints for refining 2690 atoms. 170 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2020 (Rfree = 0.000) for 2690 atoms. Found 30 (30 requested) and removed 37 (30 requested) atoms. Cycle 42: After refmac, R = 0.1812 (Rfree = 0.000) for 2677 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 43: After refmac, R = 0.1726 (Rfree = 0.000) for 2675 atoms. Found 30 (30 requested) and removed 33 (30 requested) atoms. Cycle 44: After refmac, R = 0.1658 (Rfree = 0.000) for 2667 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 45: After refmac, R = 0.1650 (Rfree = 0.000) for 2662 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.58 2.35 Round 1: 314 peptides, 9 chains. Longest chain 100 peptides. Score 0.893 Round 2: 319 peptides, 7 chains. Longest chain 77 peptides. Score 0.907 Round 3: 315 peptides, 8 chains. Longest chain 97 peptides. Score 0.899 Round 4: 313 peptides, 13 chains. Longest chain 80 peptides. Score 0.870 Round 5: 313 peptides, 10 chains. Longest chain 57 peptides. Score 0.886 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 312, Estimated correctness of the model 98.5 % 7 chains (312 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 106 A and 109 A Built loop between residues 169 A and 173 A Built loop between residues 198 A and 201 A Built loop between residues 245 A and 248 A Built loop between residues 300 A and 304 A 1 chains (326 residues) following loop building 1 chains (326 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 20732 reflections ( 99.90 % complete ) and 2475 restraints for refining 2428 atoms. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2382 (Rfree = 0.000) for 2428 atoms. Found 27 (27 requested) and removed 0 (27 requested) atoms. Cycle 47: After refmac, R = 0.2128 (Rfree = 0.000) for 2428 atoms. Found 8 (27 requested) and removed 0 (27 requested) atoms. Cycle 48: After refmac, R = 0.2055 (Rfree = 0.000) for 2428 atoms. Found 7 (27 requested) and removed 2 (27 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2024 (Rfree = 0.000) for 2428 atoms. Found 4 (27 requested) and removed 2 (27 requested) atoms. Writing output files ... TimeTaking 75.8